Machine learning model of imipenem-resistant Klebsiella pneumoniae based on MALDI-TOF-MS platform: An observational study

Yu Zeng; Chao Wang; Qing Ye; Gang Liu; Lixia Zhang; Jingjing Wan; Yu Zhu

doi:10.1002/hsr2.1108

Machine learning model of imipenem-resistant Klebsiella pneumoniae based on MALDI-TOF-MS platform: An observational study

Health Sci Rep. 2023 Apr 14;6(9):e1108. doi: 10.1002/hsr2.1108. eCollection 2023 Sep.

Authors

Yu Zeng¹, Chao Wang², Qing Ye³, Gang Liu⁴, Lixia Zhang⁴, Jingjing Wan¹, Yu Zhu⁵

Affiliations

¹ School of Chemistry and Molecular Engineering East China Normal University Shanghai China.
² Department of Clinical Laboratory First Teaching Hospital of Tianjin University of Traditional Chinese Medicine Tianjin China.
³ Department of Hepatology The Third Central Hospital of Tianjin Tianjin China.
⁴ Department of Clinical Laboratory Tianjin Haihe Hospital Tianjin China.
⁵ Department of Clinical Laboratory The Third Central Hospital of Tianjin Tianjin China.

Abstract

Background and aim: Machine learning is an important branch and supporting technology of artificial intelligence, we established four machine learning model for the drug sensitivity of Klebsiella pneumoniae to imipenem based on matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and compared their diagnostic effect.

Methods: The data of MALDI-TOF-MS and imipenem sensitivity of 174 cases of K. pneumoniae isolated from clinical specimens in the laboratory of microbiology department of Tianjin Haihe Hospital from 2019 January to 2020 December were collected. The mass spectrometry and imipenem sensitivity of 70 cases of imipenem-sensitive and 70 resistant cases were randomly selected to establish the training set model, 17 cases of sensitive and 17 cases of resistant cases were randomly selected to establish the test set model. Mass spectral peak data were subjected to orthogonal partial least squares discriminant analysis (OPLS-DA), the training set data model was established by machine learning least absolute shrinkage and selection operator (LASSO) algorithm, logistic regression (LR) algorithm, support vector machines (SVM) algorithm, neural network (NN) algorithm, the area under the curve (AUC) and confusion matrix of training set and test set model were calculated and selected by Grid search and 3-fold Cross-validation respectively, the accuracy of the prediction model was verified by test set confusion matrix.

Results: The R²Y and Q² of OPLS-DA were 0.546 and 0.0178. The AUC of the best training set and test set models were 0.9726 and 0.9100, 1.0000 and 0.8581, 0.8462 and 0.6263, 1.0000 and 0.7180 evaluated by LASSO, LR, SVM and NN model respectively. The accuracy of the LASSO, LR, SVM and NN model were 87%, 79%, 62%, and 68% in test set, respectively.

Conclusion: The LASSO prediction model of K. pneumoniae sensitivity to imipenem established in this study has a high accuracy rate and has potential clinical decision support ability.

Keywords: Klebsiella pneumoniae; artificial intelligence; imipenem; machine learning.